ArticleNucleic acids research2017
Applicability of a computational design approach for synthetic riboswitches.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Mammalian therapeutic riboswitches: Engineering and custom ligands.Molecular therapy. Nucleic acids · 2026Review
- Trends of nucleic acid - based point-of-care diagnostics for infectious diseases.Journal of biological engineering · 2026Review
- Mammalian synthetic gene circuits for biopharmaceutical development & manufacture.NPJ systems biology and applications · 2025Review
- Intelligent guide RNA: dual toehold switches for modulating luciferase in the presence of trigger RNA.Communications biology · 2024Article
- START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Review
- Developing Complex RNA Design Applications in the Infrared Framework.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Limits of experimental evidence in RNA secondary structure prediction.Frontiers in bioinformatics · 2024Article
- Elimination of editing plasmid mediated by theophylline riboswitch in Zymomonas mobilis.Applied microbiology and biotechnology · 2023Article
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- Design and Prediction of Aptamers Assisted by In Silico Methods.Biomedicines · 2023Review
- Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer.RNA biology · 2023Review
- Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?Nano today · 2022Article
- RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform.PLoS computational biology · 2022Article
- Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety.Sensors (Basel, Switzerland) · 2022Review
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Approaches in the photosynthetic production of sustainable fuels by cyanobacteria using tools of synthetic biology.World journal of microbiology & biotechnology · 2021Review
- Cell-free riboswitches.RSC chemical biology · 2021Review
- Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand-dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer structures not corresponding to the calculated MFE state.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.